All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad
is His slave and Messenger.
If those small pieces are merely minor leftovers that people do not customarily demand back – such as food scraps and the like – then it does not appear that the employee is obligated to pay for their price. Rather, this is something that is customarily overlooked. Perhaps this is what made the questioner feel uneasy about handing them over to the customer.
Lastly, we caution the questioner against blameworthy self-imposed hardship, and against intrusive whisperings (wasāwis) and dwelling on them, for this leads to great evil.
Allah knows best.